data_4XJ6
#
_model_server_result.job_id            xlK798_lDU6QGTa2KzIxOA 
_model_server_result.datetime_utc      '2024-11-24 20:29:58' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          4xj6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":504}' 
#
_entry.id    4XJ6 
#
_exptl.entry_id    4XJ6 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              507.181 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE" 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          110.61 
_cell.angle_gamma         90 
_cell.entry_id            4XJ6 
_cell.length_a            136.07 
_cell.length_b            46.3 
_cell.length_c            62.56 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4XJ6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 E N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 A OD2 ASP 129 A ASP 129 1_555 B MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? 
metalc ? metalc2 A OD1 ASP 129 A ASP 129 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? 
metalc ? metalc3 A OD2 ASP 129 A ASP 129 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? 
metalc ? metalc4 A OD2 ASP 131 A ASP 131 1_555 B MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? 
metalc ? metalc5 A OD1 ASP 131 A ASP 131 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? 
metalc ? metalc6 A OD2 ASP 191 A ASP 191 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? 
metalc ? metalc7 B MG MG . A MG 501 1_555 D O2G GH3 . A GH3 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
metalc ? metalc8 B MG MG . A MG 501 1_555 D O2B GH3 . A GH3 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? 
metalc ? metalc9 B MG MG . A MG 501 1_555 D O2A GH3 . A GH3 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
metalc ? metalc10 B MG MG . A MG 501 1_555 F O HOH . A HOH 689 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? 
metalc ? metalc11 C MG MG . A MG 502 1_555 F O HOH . A HOH 691 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? 
#
_chem_comp.formula           'C10 H16 N5 O13 P3' 
_chem_comp.formula_weight    507.181 
_chem_comp.id                GH3 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_chem_comp.pdbx_synonyms     ? 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
PG O1G GH3 doub 83 n n 
PG O2G GH3 sing 84 n n 
PG O3G GH3 sing 85 n n 
PG O3B GH3 sing 86 n n 
O2G HOG2 GH3 sing 87 n n 
O3G HOG3 GH3 sing 88 n n 
O3B PB GH3 sing 89 n n 
PB O1B GH3 doub 90 n n 
PB O2B GH3 sing 91 n n 
PB O3A GH3 sing 92 n n 
O2B HOB2 GH3 sing 93 n n 
O3A PA GH3 sing 94 n n 
PA O1A GH3 doub 95 n n 
PA O2A GH3 sing 96 n n 
PA O5' GH3 sing 97 n n 
O2A HOA2 GH3 sing 98 n n 
O5' C5' GH3 sing 99 n n 
C5' C4' GH3 sing 100 n n 
C5' H5' GH3 sing 101 n n 
C5' "H5''" GH3 sing 102 n n 
C4' O4' GH3 sing 103 n n 
C4' C3' GH3 sing 104 n n 
C4' H4' GH3 sing 105 n n 
O4' C1' GH3 sing 106 n n 
C3' C2' GH3 sing 107 n n 
C3' "H3'2" GH3 sing 108 n n 
C3' H3' GH3 sing 109 n n 
C2' O2' GH3 sing 110 n n 
C2' C1' GH3 sing 111 n n 
C2' H2' GH3 sing 112 n n 
O2' HO2' GH3 sing 113 n n 
C1' N9 GH3 sing 114 n n 
C1' H1' GH3 sing 115 n n 
N9 C8 GH3 sing 116 n y 
N9 C4 GH3 sing 117 n y 
C8 N7 GH3 doub 118 n y 
C8 H8 GH3 sing 119 n n 
N7 C5 GH3 sing 120 n y 
C5 C6 GH3 sing 121 n n 
C5 C4 GH3 doub 122 n y 
C6 O6 GH3 doub 123 n n 
C6 N1 GH3 sing 124 n n 
N1 C2 GH3 sing 125 n n 
N1 HN1 GH3 sing 126 n n 
C2 N2 GH3 sing 127 n n 
C2 N3 GH3 doub 128 n n 
N2 HN21 GH3 sing 129 n n 
N2 HN22 GH3 sing 130 n n 
N3 C4 GH3 sing 131 n n 
#
_atom_sites.entry_id                     4XJ6 
_atom_sites.fract_transf_matrix[1][1]    0.007349 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002764 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.021598 
_atom_sites.fract_transf_matrix[2][3]    0 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.017078 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
B 2 MG A 1 501 1 MG MG . 
C 2 MG A 1 502 2 MG MG . 
D 3 GH3 A 1 503 1 GH3 GTP . 
E 3 GH3 A 1 504 1 GH3 GTP . 
F 4 HOH A 1 601 28 HOH HOH . 
F 4 HOH A 2 602 84 HOH HOH . 
F 4 HOH A 3 603 36 HOH HOH . 
F 4 HOH A 4 604 135 HOH HOH . 
F 4 HOH A 5 605 50 HOH HOH . 
F 4 HOH A 6 606 5 HOH HOH . 
F 4 HOH A 7 607 41 HOH HOH . 
F 4 HOH A 8 608 29 HOH HOH . 
F 4 HOH A 9 609 143 HOH HOH . 
F 4 HOH A 10 610 52 HOH HOH . 
F 4 HOH A 11 611 83 HOH HOH . 
F 4 HOH A 12 612 119 HOH HOH . 
F 4 HOH A 13 613 43 HOH HOH . 
F 4 HOH A 14 614 115 HOH HOH . 
F 4 HOH A 15 615 70 HOH HOH . 
F 4 HOH A 16 616 65 HOH HOH . 
F 4 HOH A 17 617 101 HOH HOH . 
F 4 HOH A 18 618 157 HOH HOH . 
F 4 HOH A 19 619 138 HOH HOH . 
F 4 HOH A 20 620 14 HOH HOH . 
F 4 HOH A 21 621 39 HOH HOH . 
F 4 HOH A 22 622 153 HOH HOH . 
F 4 HOH A 23 623 128 HOH HOH . 
F 4 HOH A 24 624 105 HOH HOH . 
F 4 HOH A 25 625 159 HOH HOH . 
F 4 HOH A 26 626 82 HOH HOH . 
F 4 HOH A 27 627 48 HOH HOH . 
F 4 HOH A 28 628 165 HOH HOH . 
F 4 HOH A 29 629 155 HOH HOH . 
F 4 HOH A 30 630 176 HOH HOH . 
F 4 HOH A 31 631 4 HOH HOH . 
F 4 HOH A 32 632 7 HOH HOH . 
F 4 HOH A 33 633 10 HOH HOH . 
F 4 HOH A 34 634 11 HOH HOH . 
F 4 HOH A 35 635 13 HOH HOH . 
F 4 HOH A 36 636 15 HOH HOH . 
F 4 HOH A 37 637 16 HOH HOH . 
F 4 HOH A 38 638 18 HOH HOH . 
F 4 HOH A 39 639 21 HOH HOH . 
F 4 HOH A 40 640 22 HOH HOH . 
F 4 HOH A 41 641 25 HOH HOH . 
F 4 HOH A 42 642 26 HOH HOH . 
F 4 HOH A 43 643 32 HOH HOH . 
F 4 HOH A 44 644 33 HOH HOH . 
F 4 HOH A 45 645 34 HOH HOH . 
F 4 HOH A 46 646 35 HOH HOH . 
F 4 HOH A 47 647 37 HOH HOH . 
F 4 HOH A 48 648 42 HOH HOH . 
F 4 HOH A 49 649 45 HOH HOH . 
F 4 HOH A 50 650 49 HOH HOH . 
F 4 HOH A 51 651 51 HOH HOH . 
F 4 HOH A 52 652 56 HOH HOH . 
F 4 HOH A 53 653 57 HOH HOH . 
F 4 HOH A 54 654 60 HOH HOH . 
F 4 HOH A 55 655 61 HOH HOH . 
F 4 HOH A 56 656 64 HOH HOH . 
F 4 HOH A 57 657 66 HOH HOH . 
F 4 HOH A 58 658 67 HOH HOH . 
F 4 HOH A 59 659 68 HOH HOH . 
F 4 HOH A 60 660 69 HOH HOH . 
F 4 HOH A 61 661 71 HOH HOH . 
F 4 HOH A 62 662 72 HOH HOH . 
F 4 HOH A 63 663 76 HOH HOH . 
F 4 HOH A 64 664 77 HOH HOH . 
F 4 HOH A 65 665 79 HOH HOH . 
F 4 HOH A 66 666 80 HOH HOH . 
F 4 HOH A 67 667 85 HOH HOH . 
F 4 HOH A 68 668 88 HOH HOH . 
F 4 HOH A 69 669 89 HOH HOH . 
F 4 HOH A 70 670 91 HOH HOH . 
F 4 HOH A 71 671 92 HOH HOH . 
F 4 HOH A 72 672 93 HOH HOH . 
F 4 HOH A 73 673 103 HOH HOH . 
F 4 HOH A 74 674 108 HOH HOH . 
F 4 HOH A 75 675 111 HOH HOH . 
F 4 HOH A 76 676 113 HOH HOH . 
F 4 HOH A 77 677 121 HOH HOH . 
F 4 HOH A 78 678 125 HOH HOH . 
F 4 HOH A 79 679 129 HOH HOH . 
F 4 HOH A 80 680 131 HOH HOH . 
F 4 HOH A 81 681 133 HOH HOH . 
F 4 HOH A 82 682 134 HOH HOH . 
F 4 HOH A 83 683 139 HOH HOH . 
F 4 HOH A 84 684 141 HOH HOH . 
F 4 HOH A 85 685 147 HOH HOH . 
F 4 HOH A 86 686 166 HOH HOH . 
F 4 HOH A 87 687 170 HOH HOH . 
F 4 HOH A 88 688 171 HOH HOH . 
F 4 HOH A 89 689 172 HOH HOH . 
F 4 HOH A 90 690 173 HOH HOH . 
F 4 HOH A 91 691 174 HOH HOH . 
F 4 HOH A 92 692 175 HOH HOH . 
F 4 HOH A 93 693 177 HOH HOH . 
F 4 HOH A 94 694 178 HOH HOH . 
F 4 HOH A 95 695 179 HOH HOH . 
F 4 HOH A 96 696 180 HOH HOH . 
F 4 HOH A 97 697 181 HOH HOH . 
F 4 HOH A 98 698 182 HOH HOH . 
F 4 HOH A 99 699 183 HOH HOH . 
F 4 HOH A 100 700 184 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 O O3A GH3 . . . E 3 13.796 2.479 26.433 1 51.52 ? O3A GH3 504 A 1 
HETATM 2 P PA GH3 . . . E 3 13.676 4.08 26.543 1 70.09 ? PA GH3 504 A 1 
HETATM 3 O O1A GH3 . . . E 3 12.978 4.601 25.31 1 73.91 -1 O1A GH3 504 A 1 
HETATM 4 O O2A GH3 . . . E 3 15.021 4.742 26.738 1 65.84 -1 O2A GH3 504 A 1 
HETATM 5 O O5' GH3 . . . E 3 12.721 4.307 27.819 1 39.6 ? O5' GH3 504 A 1 
HETATM 6 C C5' GH3 . . . E 3 11.874 3.273 28.27 1 37.03 ? C5' GH3 504 A 1 
HETATM 7 C C4' GH3 . . . E 3 10.936 3.827 29.331 1 32.36 ? C4' GH3 504 A 1 
HETATM 8 O O4' GH3 . . . E 3 11.178 5.207 29.498 1 37.56 ? O4' GH3 504 A 1 
HETATM 9 C C3' GH3 . . . E 3 9.463 3.701 28.98 1 26.57 ? C3' GH3 504 A 1 
HETATM 10 C C2' GH3 . . . E 3 8.84 4.933 29.619 1 27.19 ? C2' GH3 504 A 1 
HETATM 11 O O2' GH3 . . . E 3 8.312 4.611 30.885 1 25.68 ? O2' GH3 504 A 1 
HETATM 12 C C1' GH3 . . . E 3 9.986 5.915 29.792 1 32.32 ? C1' GH3 504 A 1 
HETATM 13 N N9 GH3 . . . E 3 9.873 6.966 28.771 1 24.39 ? N9 GH3 504 A 1 
HETATM 14 C C8 GH3 . . . E 3 10.503 6.916 27.554 1 18.49 ? C8 GH3 504 A 1 
HETATM 15 N N7 GH3 . . . E 3 10.198 8.037 26.871 1 24.16 ? N7 GH3 504 A 1 
HETATM 16 C C5 GH3 . . . E 3 9.394 8.805 27.64 1 23.93 ? C5 GH3 504 A 1 
HETATM 17 C C6 GH3 . . . E 3 8.81 10.041 27.408 1 24.93 ? C6 GH3 504 A 1 
HETATM 18 O O6 GH3 . . . E 3 9.002 10.617 26.338 1 23.11 ? O6 GH3 504 A 1 
HETATM 19 N N1 GH3 . . . E 3 8.017 10.614 28.377 1 25 ? N1 GH3 504 A 1 
HETATM 20 C C2 GH3 . . . E 3 7.811 9.953 29.57 1 22.22 ? C2 GH3 504 A 1 
HETATM 21 N N2 GH3 . . . E 3 7.042 10.518 30.501 1 20.21 ? N2 GH3 504 A 1 
HETATM 22 N N3 GH3 . . . E 3 8.398 8.719 29.794 1 24.16 ? N3 GH3 504 A 1 
HETATM 23 C C4 GH3 . . . E 3 9.179 8.15 28.844 1 20.95 ? C4 GH3 504 A 1 
#
_model_server_stats.io_time_ms              79 
_model_server_stats.parse_time_ms           23 
_model_server_stats.create_model_time_ms    50 
_model_server_stats.query_time_ms           1050 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           23 
#